Jeanson is now finding a reason to ignore neanderthal DNA

Hi Dave
Do you have a model of how mutations accumulate in a single population (humans) which is what I think you call the substitution rate?

He is using the mutation rate as most population genetic models do. He is testing this observed accumulation (spread) against a population curve independently derived. At the time of the video you did not understand the basis of this curve.

I appreciate you engaging with Nathaniel.

Why is the scaling so close in the 3 models? Why when you eliminate the Neanderthals data does the curve fit.

I donā€™t know. What I know is that the assumption that the curves ought to fit is wrong, and there is much evidence that the root ought to be where science puts it rather than where Jeanson puts it. How can he and you ignore all that evidence? (Hypothesis: you accept only what fits your assumptions and reject the rest.)

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What evidence do you think he is ignoring. He is building a model based on a 4500 year old human population. The model appears to work against an independent criteria.

The substitution rate is number of substitution mutations that occur per offspring. I think you are looking for the fixation rate.

In my experience, pop gen models use the mutation rate to calculate the fixation rate, and then use the fixation rate to predict the difference between and within populations.

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That a curve should fit when data that makes it not do so, is discarded, is an enduring mystery in creationist ā€œscience.ā€

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  1. If they were degraded, they would not be highly correlated with each other. In other words, the specific sites that degrade would be uncorrelated. We would see extremely divergent sequences from each other, not highly clustered clades.

  2. The homologous sequences within the diploid genomes would be highly divergent, increasing heterozygosity. Instead, we find evidence of inbreeding. Degradation is not going to increase homozygosity.

  3. We know, very precisely, the rate at which cytosine deaminates to uracil, which allows us to separate truly ancient DNA (highly enriched in uracil) from modern contaminants. The degree of uracil enrichment is what we would expect from DNA of the ages in question.

To date, Jeanson has addressed none of these points. The first two are direct falsifications of the alternative hypothesis that these sequences are too degraded to be reliable, and the third is a direct falsification of the alternative hypothesis that these are actually modern sequences.

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Think about what youā€™re saying here. A 4500 year old human population puts the origin at 2500 BC. This is younger than many cities and civilizations, younger than the pyramids, much, much younger than human remains and sites all over the world, including the Americas. Jeanson ignores almost all the data because he doesnā€™t like it. You appear to be OK with that and are willing to do the same. Are you actually willing to go full YEC?

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My name is Dan.

Nobody applies a mutation rate back infinitely for TMRCA calculations. Because natural selection is real. And also because heā€™s not distinguishing between germline and somatic mutations, and ignoring germline bottlenecks, etc. But mostly because the sequences in question (mitochondrial DNA and Y chromosome) are very clearly subject to purifying selection. And when you have selection, you also weed out linked neutral variants. Population geneticists understand this. Jeanson ignores it.

Mutation accumulation does not equal ā€œspreadā€ (by which I think you mean an increasing number of branches). @Herman_Mays has explained at length why this is the case, and @thoughtful drew it out by hand and got it. Iā€™m not sure why Jeanson doesnā€™t understand the problem.

At the time of our conversation, I didnā€™t recall off the top of my head the content of one of his AiG ā€œpapersā€ from the title. But not 30 seconds later in the video I described the technique and Jeanson confirmed that I was correct.

I wish he would do more engaging. Heā€™s declined to continue our conversation.

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As you keep pressing this point, one possibility is that Jeanson worked backwards from his desired curve, and culled the data and parameterized the model to make it fit. He essentially said as much when he rejected ancient DNA - not just Neanderthal, but all ancient DNA - and used the mutation rate as fixation. He was also selective in the portion of his farcical independent test data, as he just buzz saws off the population curve where it conflicts with his YEC dogma. Here is a test. If your inference conflicts with recorded human history, your idea is wrong and it is a waste to give it further consideration.

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Itā€™s false he ignores the data because he does not like it he is building his models independently. I asked him about the objections you raised and he referred me to other YEC scientists.

Your first two points I agree with if the are truly representative of the Neathandral Y chromosome.

How do you reconcile this paper with your claims.

Jeanson excludes the data from his independent model because it doesnā€™t fit his independent model.

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You misunderstand.

When I say we see well-defined clades, Iā€™m talking about within Neanderthal sequences. They form a robust clade. They are highly divergent from extant H. sapiens (indicative of a TMRCA of H. sapiens and Neanderthals far in excess of that for all extant H. sapiens Y chromosomes), but not from each other. Neanderthal sequences are highly similar to each other, which, again, is a direct falsification of the hypothesis that the sequences are too degraded to be reliable.

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Ancient H. sap genomes have also been sequenced:

If the age of the samples makes H. sap sequence change into Neanderthal sequence, then how can this genome sequence be explained?

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My opinion is that he sees those curves working, and he likes them. :slightly_smiling_face: He needs to see them not working for one of his predictions.

As @dsterncardinale mentioned in the thread earlier after I drew out some scenarios and saw the curves do not always work, I also basically wrote they could possibly work as a rough approximation with enough sampling and the right root. But he doesnā€™t have enough evidence yet to show thatā€™s the case. He either needs a simulation or much more evidence that fits predictions. What he has now could just be coincidental and spurious.

Iā€™m curious if @evograd has any relevant data from the programming he was doing for exponential growth scenarios. I was looking forward to that. :slightly_smiling_face: If you have the time to indulge us (I mean, me) haha.

You are accurate but not as much as you think. My biggest beef is that you frequently donā€™t distinguish between whether youā€™re referring to mtDNA or the y-chromosome when the evidence and so the arguments can be completely different. For some reason I was really confused and thought the substitution rate had to do with drift. Maybe you have referred to selection. But I didnā€™t get it. Not necessarily your fault. Just letting you know.

Did anyone see that Rob Carter put out a video a day or two ago? He was complimentary of Jeanson but the title of the video was that there was no molecular clock. His explanations were very helpful. I like that they donā€™t agree because more actually gets uncovered that way.

Anyway, he mentioned that North American settlement by Q has been used an anchor point for dating the mainstream phylogeny. (I donā€™t know if Iā€™m explaining that right).

I think the same thing could be done for a creationist y-chromosome tree. At least if a hypothesis I barely hinted at is correctā€¦ I hinted a little in my conversations with @Tim that after some research I didnā€™t agree with Jeansonā€™s ideas about the recent history of R1b in Europe. Instead, I think it is French (who immigrated from Central Asia much earlier.) Mainstream science thinks the western European origin is Spain and radiates from Spain probably because itā€™s high in the Basque country. But I think itā€™s radiates from southern France because of French Huguenot persecution. Over almost few centuries, but especially in the 1600s they fled to Basque country, northern Italy, the Netherlands, England, Ireland, the Americas, Australia, South Africa, etc, sometimes a generation immigrating to one area and the next generation moving on. It was basically genocidal and those people who immigrated from France had lots of kids, haha. The R1b split seems to be somewhere in the line of Henry IV (because of a few papers confirming that). The idea seems plausible anyway. And people took their surnames from places they lived so many related people had different names at the time. And many of the persecuted were educated and from nobility, so R1b could be Capetian and kingly. I think this hypothesis is plausible but I didnā€™t feel like I had the time to defend it through more research. I definitely donā€™t now, haha. The start of school made life even crazier. I just wanted to share this if there are any creationist lurkers who want to take up the hypothesis. Itā€™s another way to approach the y-chromosome phylogeny whether the clock works or not. It seems like the genealogies to find the R1b ancestor should be out there. Itā€™s always hard to tell with non-paternity eventsā€¦but perhaps enough data could be accumulated. Either way, fun to think aboutā€¦and a very different explanation than an evolutionary phylogeny!!

When you use the wrong methodology combined with the wrong data, you get an artificial result, regardless if it appears to have a high correlation or not. And unsurprisingly, when you use the wrong methodology combined with the right data, you get an obviously wrong result.

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I agree. Jeanson is building his models independently of scientific data.

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So word salad, then.

So he has other people who ignore data for him. Sure.

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I got it but based on this I would suspect higher similarity to H.S. Y chromosome if they indeed share a common ancestor. Can you point me in the direction of papers pointing to sequence similarity? Are they Y chromosome sequences?